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Basic Building Blocks: Proteins• Largest variety of biomolecules• Most of the weight of cells, aside from water• Basic unit is amino acid • Form of amino acid•Simplest is glycine
with R = H• All others are asymmetrictwo stereoisomers L & Dwith mainly L naturally occuring
Human Genome Project Facts• Human DNA codes about 30,000 genes
(vs. fruit flies:13,500 and C. elegans: 19,000)
• These genes represent only ~ 1% of DNA – lots of coding for control & transcription factors
• Average human protein has ~450 amino acids
• One of the largest proteins is titin (27,000 amino acids in a single chain)
Protein Functions• Motion & locomotion of cells/organism
(contractile proteins)• Catalysis of all biochemical reactions
(enzymes)• Structure of cells and extracellular matrix
(e.g. collagens)• Receptors for hormones/ signaling
molecules• Transcription factors• Etc.
Example Protein (H-2K) - Structure• This antigen displays many
features of proteins– Two polypeptide chains– Longer heavy chain has 5 domains –
3 extracellular, one transmembrane, and one cytoplasmic – it is called an integral membrane protein
– Smaller polypeptide chain is attached to heavy chain by H bonds (no covalent bonds) – it is a peripheral membrane protein
– The dark bars are disulfide bridges (S-S)
– Two short branched sugars are on the left making this a glycoprotein (sugar + protein compex)
The view seen here does not show its real 3D arrangement
Look in PDB
Types of amino acids• Classify aa by various criteria – each has
3 letter or 1 letter code
• 3 have ring-structures – important in fluorescence
• All are ampholytes (+/- charge depending on pH)
Amino Acids
Digression: pH ideas• pH = -log[H+]• Neutrality when [H+]=[OH-]=10-7 M• Higher pH – basic; lower – acidic• Simple idea: H2O OH- + H+
• Dissociation constant K
where G = free energy per mole of bond formation; with [H2O] = 55 M ~ constant
So K’ = [H+][OH-] = 10-14 and pK = -log K in general
/
2
[ ][ ]
[ ]G kTH OH
K eH O
pH and pK• Each charged group has a pK
• For proteins, e.g., – COOH COO- + H+ pK 2.34
– NH3+ NH2 + H+ pK 9.69
– R group dissociation also
If pH > pK more basic form
If pH < pK more acidic form
Different forms predominate at different pH - polyelectrolyte
Example: Titration of alanine
• Different forms at different pH
• Alanine has R = CH3
• pI = isoelectric point =
pH at which neutral
Peptide bond• Amino acids link together to form a
continuous linear chain = backbone of protein
Primary Structure• With even only 10 a.a. long – number of possible
polypeptides (decamers) = 2010 = 1010x210 ~ 1013
• Amino acid composition – not sequence – can be automatically determined by aa analyzer to give % composition
• General features of 1o structure:– Most polypeptide chains are 100 – 500 aa; smallest
25 – 100, largest 3000– Some proteins have more than 1 chain – held
together by weaker non-covalent bonds– Protein data bank – on-line
Facts about 1o structure• Wide variation in composition
• Certain aa are fairly rare
(methionine, Tryptophan)
• Ala, Leu very common
• Many proteins contain
other molecules, including
carbohydrates, metal ions
(Ca, Fe, Zn, Cu)
Metal Ions in Proteins
Secondary Structure (2o) of Proteins
• Backbone of protein chain has
series of rotatable bonds. Two
angles describe possible
rotations of each peptide
• Rotations about these bonds
lead to certain allowed
structures – or stable
conformations
Ramachandran Diagram• A number of helices and sheets are
possible
-helix + -sheet
- Right-handed
- 3.6 aa per turn
- R groups outside
- H bond between
-NH and –C=O
4 aa apart pointing
along axis
-Pairs of chains lying
side by side
- Stabilized by H bonds
More -helix, sheet, triple helix
Collagen triple helix
All proteins consist of regions of 2nd structure w/ random coil connections
Prediction of structure• Based on knowing aa
sequence, we are able to predict -helix, -sheet regions
• For example:residues 1-36 in histone have 12 + charges – able to bind to neg. charges on d-s DNA
• For example: glycophorin from human RB cells spans membrane from 73 – 95 non-polar region
Prediction of Structure II
Protein Folding Problem• Big Question is: If you know the primary
sequence of aa can you predict the 3-D structure of a protein? [Protein-folding problem – one of challenges]
• Can occur spontaneously – involves basic electrical interactions that we’ll study soon– Co-valent bonds along backbone– H-bonds – weaker, directional– Van der Waals – non-specific attractive– Hydrophobic/ hydrophilic – entropy driven
forces
Tertiary Structure (3o)
Interleukin-1ß-converting enzyme
• Human ICE-protease
• All proteins consist of 2o structure regions connected by random coil
Protein Domains• Tertiary structure of proteins is built up from domains• Each domain has a separate function to perform – for
example:– Binding a small ligand– Spanning the plasma membrane– Containing a catalytic site– DNA binding (transcription factors)– Providing a binding surface for another protein
• Often each domain is encoded by a separate exon in the gene encoding that protein – this correspondence is most likely to occur in recently-evolved proteins (exon shuffling idea to generate new proteins using established domains – like Lego pieces)
Fibrous Proteins• Two major classes of proteins
based on 3o Structure– Fibrous – fiber-like, includes
• Keratins – in hair, horns, feathers, wool
• Actin – muscle thin filaments, cells
• Collagen – connective tissue
Often these are polymers made up from monomer subunits and form all helices and/or all sheets (e.g. silk) Actin filament made
from monomers
Globular Proteins
• Second class is globular – most enzymes, hormones, transport proteins – folded up structure
General Properties of 3o Structure1. Lowest energy states are most stable 3o
structures
2. Charged residues are on surface or exposed clefts
3. Non-polar (hydrophobic) residues are internal
4. Nearly all possible H-bonds form
Quaternary (4o) Structure• Multiple sub-units bound together non-
covalently
• Canonical example is hemoglobin:
Cooperative Binding by Hemoglobin• Fe in the heme group binds oxygen – separately,
each of 4 hemes binds O2 as in myoglobin – 4 together bind O2 cooperatively – Allosteric conformational change
Sigmoidal binding curve indicates cooperativity
TMV – 4o structure
Packing Density of Proteins• How filled is volume of protein?
• Quantitative measure = packing density =
• For continuous solid PD = 1
• For close packed spheres PD = 0.74
• For close packed cylinders PD = 0.91
• For ribonuclease S, PD = 0.75
volume enclosed by all van der Waals RPD
total volume
Two Other Classes of Biomolecules- Polysaccharides + Lipids
• Polysaccharides (carbohydrates)– Monosaccharide – eg glucose– Disaccharide – eg lactose– Polymers of sugars – M ~ 104 – 107 Da
+
lactose
Polysaccharides - con’t
• Glucose can polymerize into 3 types of polymers– Starch- polymers of glucose – metabolic
– Glycogen- ditto, but with more shorter
branching –also metabolic- stores glucose– Cellulose – most prevalent biomolecule -
structural
Lipids• Very diverse family – all
insoluble in water/ rich in hydrocarbons
• Includes fatty acids, steroids, phosphoglycerides/phospholipids in membranes
• Polar head group = fatty acid tail with 12 – 24 C’s in tail
cholesterol
bilayer micelle
Vesicle (unilamellar)